通过MM/PBSA等方法计算结合能(ΔG),发现YN14-H-KRASG12C-VHL复合物的ΔG为−158.12 kJ/mol,相较于其他降解剂,YN14-H促进KRASG12C和VHL形成更稳定的相互作用,诱导的三元复合物稳定性最强。进一步利用微尺度热泳(MST)、AlphaScreen(AS)及细...
RMSD of the C-alpha carbon atoms of MMP-2 (PDB code: 1HOV) for the equilibration trajectories.Ilenia GiangrecoGianluca LattanziOrazio NicolottiMarco CattoAntonio LaghezzaFrancesco LeonettiAngela StefanachiAngelo Carotti
微调代码,见finetuning_lora.py,核心部分如下: model = ChatGLMForConditionalGeneration.from_pretrained(args.model_dir) config = LoraConfig(r=args.lora_r, lora_alpha=32, target_modules=["query_key_value"], lora_dropout=0.1, bias="none", task_type="CAUSAL_LM", inference_mode=False, ) model...
The coiled-coil dimer of the S143F mutant lamin showed long alpha-helix bending at linker L1 between coil 1a and coil 1b (Fig. 1). Superposition of the S143F mutant and A:B or C:D coiled-coil dimers of the wild-type lamin structures have a root-mean-square deviation (RMSD) of ...
d) build full-atomic model from C-alpha trace model > ModRefiner.pl 4 ID MD IM RM ON ID: the path of the C-I-TASSER package, e.g. '/home/yourname/C-I-TASSER-1.0' MD: directory which contains the initial model, e.g. '/home/yourname/C-I-TASSER/5.0/example' IM: the initial...
(3 to 5 nm,Fig. 4andTable 2). Likewise, the bimane at site 139 was quenched by 5-doxyl-stearic acid in the pre-complex (14%) even though no blue-shift was observed (Table 2). In the crystal structure of the Ops*–arrestin-1 complex, the alpha carbons of both sites 251 and ...
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Figure 9. Differences in Average RMSD (C-Alpha Atoms) between 1C4-Mannosylated RNase and “Apo” RNase 2 A slight reduction in RMSD occurs for Trp7 (highlighted with gray background), but a significant decrease in RMSD is evident for the insertion loop (residues 114–124, highlighted with ...
EVO maintained stability within a range of 5.5–6.5 Å from C/EBP-β, while the final RMSD of the ligand stabilized around 8.5 Å after fluctuations (Fig. 8C). The results showed that there was a certain change in the initial conformation of EVO and C/EBP - β. After ...
The EOM models were then processed using the PD2 ca2main program to generate models in which the residues were replaced with a C-alpha backbone39. The models prepared this way were used as a starting pool in the Gajoe program (version 2.0)38 in the ATSAS package; this program selects a...